Evaluate gene sets identified by SDAN
Wei Sun
2024-07-10
Setup
Check enrichment of gene sets
Read in gene info and gene set assignments
file_tag = sprintf("%s_%s", cell_type_name, graph_weight)
assayed_genes = scan(sprintf("output/gene_list_%s.txt", file_tag),
what = character(), sep="\n")
gene_sets = scan(sprintf("output/name_s_%s.txt", file_tag),
what = character(), sep="\n")
gene_sets = sapply(gene_sets, strsplit, split=",")
n_genes = sapply(gene_sets, length)
names(n_genes) = NULL
summary(n_genes)## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 39.0 42.0 43.0 42.9 44.0 45.0## [1] 40## [1] 39 40 41 41 41 41 41 41 41 42 42 42 42 42 43 43 43 43 43 43 43 43 44 44 44
## [26] 44 44 44 44 44 44 44 44 44 44 44 45 45 45 45Find gene symbols
Find gene symbols from bioMart.
All the gene symbols that can be found in bioMart are
consistent with what we have. So no need to run it.
ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl")
gene_BM = getBM(attributes = c("hgnc_symbol", "external_gene_name"),
filters = "external_gene_name",
values = assayed_genes,
mart = ensembl)
length(assayed_genes)
dim(gene_BM)
gene_BM[1:2,]
table(assayed_genes %in% gene_BM$external_gene_name)
t1 = table(gene_BM$external_gene_name)
dup = names(t1)[t1 > 1]
gene_BM[gene_BM$external_gene_name %in% dup,]
table(gene_BM$hgnc_symbol == gene_BM$external_gene_name)
w2kp = which(gene_BM$hgnc_symbol != gene_BM$external_gene_name)
gene_BM[w2kp,]Find gene symbols using the alias2Symbol function from
limma.
a2s = rep(NA, length(assayed_genes))
for(i in 1:length(assayed_genes)){
gi = assayed_genes[i]
ai = alias2Symbol(gi)
if(length(ai) > 1){
print(gi)
print(ai)
}
a2s[i] = ai[1]
}## [1] "MPP6"
## [1] "MPHOSPH6" "PALS2"##
## FALSE TRUE
## 1643 357##
## FALSE TRUE <NA>
## 21 1622 357gene_info = data.table(sym_in_data = assayed_genes, sym_limma = a2s)
gene_info[sym_in_data != sym_limma,]## sym_in_data sym_limma
## 1: BTBD11 ABTB3
## 2: LINC01006 RNF32-DT
## 3: LINC01185 REL-DT
## 4: ZRANB2-AS2 ZRANB2-DT
## 5: LINC00271 AHI1-DT
## 6: RFX3-AS1 RFX3-DT
## 7: COX10-AS1 COX10-DT
## 8: SUCLG2-AS1 SUCLG2-DT
## 9: C5orf17 LINC02899
## 10: OSMR-AS1 OSMR-DT
## 11: C8orf37-AS1 CFAP418-AS1
## 12: CTB-178M22.2 TENM2-AS1
## 13: LINC00637 PPP1R13B-DT
## 14: MPP6 MPHOSPH6
## 15: C7orf61 SPACDR
## 16: C3orf35 APRG1
## 17: HRAT92 PDGFA-DT
## 18: LINC00884 ATP13A3-DT
## 19: LINC01137 ZC3H12A-DT
## 20: TMEM161B-AS1 TMEM161B-DT
## 21: MAFG-DT MILIP
## sym_in_data sym_limmagene_info[, gene_symbol := sym_in_data]
gene_info[which(sym_in_data != sym_limma & (gene_symbol != "MT-CO2")),
gene_symbol := sym_limma]
dim(gene_info)## [1] 2000 3## sym_in_data sym_limma gene_symbol
## 1: CD38 CD38 CD38
## 2: PRKAR2B PRKAR2B PRKAR2B
## 3: ASB4 ASB4 ASB4
## 4: USH1C USH1C USH1C
## 5: ARHGAP44 ARHGAP44 ARHGAP44## t1
## 1
## 2000Prepare gene set information
Gene set annotations (by gene symbols) were downloaded from MSigDB website.
gmtfile = list()
gmtfile[["reactome"]] = "../Annotation/c2.cp.reactome.v2023.2.Hs.symbols.gmt"
gmtfile[["go_bp"]] = "../Annotation/c5.go.bp.v2023.2.Hs.symbols.gmt"
pathways = list()
for(k1 in names(gmtfile)){
pathways[[k1]] = gmtPathways(gmtfile[[k1]])
}
names(pathways)## [1] "reactome" "go_bp"## reactome go_bp
## 1692 7647Filter gene sets for size between 10 and 500.
## $reactome
## 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
## 5.0 7.0 9.0 12.0 17.0 23.0 31.0 44.0 71.8 120.9 1463.0
##
## $go_bp
## 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
## 5.0 6.0 8.0 10.0 14.0 19.0 29.0 46.0 80.8 183.0 1966.0Conduct enrichment analysis
## [1] 2000 3## sym_in_data sym_limma gene_symbol
## 1: CD38 CD38 CD38
## 2: PRKAR2B PRKAR2B PRKAR2B## [1] 36517 9## gene_ids feature_is_filtered feature_name feature_reference
## 1: ENSG00000000003 FALSE TSPAN6 NCBITaxon:9606
## 2: ENSG00000000005 FALSE TNMD NCBITaxon:9606
## feature_biotype n_cells_by_counts mean_counts pct_dropout_by_counts
## 1: gene 6900 0.118699020 90.14412
## 2: gene 161 0.002485395 99.77003
## total_counts
## 1: 8310
## 2: 174## [1] 2000##
## TRUE
## 2000##
## FALSE TRUE
## 34517 2000gene_dat$selected = 0
gene_dat$selected[match(gene_info$sym_in_data, gene_dat$feature_name)] = 1
table(gene_dat$selected)##
## 0 1
## 34517 2000## $`0`
## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 0.00857 90.44551 99.20296 90.72478 99.93429 100.00000
##
## $`1`
## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 0.00 60.04 81.87 72.81 92.88 97.99gene_info = merge(gene_info, gene_dat, by.x="sym_in_data",
by.y="feature_name", all.x = TRUE, all.y = FALSE)
dim(gene_info)## [1] 2000 12## sym_in_data sym_limma gene_symbol gene_ids feature_is_filtered
## 1: A2M A2M A2M ENSG00000175899 FALSE
## 2: A2ML1-AS1 A2ML1-AS1 A2ML1-AS1 ENSG00000256661 FALSE
## feature_reference feature_biotype n_cells_by_counts mean_counts
## 1: NCBITaxon:9606 gene 5826 0.1207987
## 2: NCBITaxon:9606 gene 11030 0.2138297
## pct_dropout_by_counts total_counts selected
## 1: 91.67821 8457 1
## 2: 84.24488 14970 1max_n2kp = 10
goseq_res = NULL
for(k in 1:length(gene_sets)){
if(length(gene_sets[[k]]) < 10) { next }
print(k)
set_k = paste0("set_", k)
print(gene_sets[[k]])
genes = gene_info$sym_in_data %in% gene_sets[[k]]
names(genes) = gene_info$gene_symbol
table(genes)
pwf = nullp(genes, "hg38", "geneSymbol",
bias.data = 100 - gene_info$pct_dropout_by_counts)
for(k1 in names(pathways)){
p1 = pathways[[k1]]
res1 = goseq(pwf, "hg38", "geneSymbol",
gene2cat=goseq:::reversemapping(p1))
res1$FDR = p.adjust(res1$over_represented_pvalue, method="BH")
nD = sum(res1$FDR < 0.05)
if(nD > 0){
res1 = res1[order(res1$FDR),][1:min(nD, max_n2kp),]
res1$category = gsub("REACTOME_|GOBP_", "", res1$category)
res1$category = gsub("_", " ", res1$category)
res1$category = tolower(res1$category)
res1$category = substr(res1$category, start=1, stop=81)
goseq_res[[set_k]][[k1]] = res1
}
}
}## [1] 1
## [1] "MYO16" "AMPH" "PPEF1" "SGK2" "FRK" "SIPA1L2"
## [7] "APOC1" "MON1A" "CES2" "ZNF497" "RAB39A" "IL1RAPL2"
## [13] "ITGA3" "CCDC124" "SYN1" "NGEF" "PPP1R15A" "CASS4"
## [19] "EPHB6" "SUSD1" "CHD5" "DUSP1" "KIAA1217" "LRRC4B"
## [25] "HAVCR2" "MICAL1" "ARHGAP26" "SNTG1" "SLC43A1" "TBX6"
## [31] "FSIP1" "CNKSR3" "FBXO32" "C2CD2" "DHRSX" "REPS2"
## [37] "SYNM" "ANKS1B" "HAUS7"
## [1] 2
## [1] "ANKRD24" "SPATA6L" "TFAP2E" "DNAH12"
## [5] "HDHD5-AS1" "MAMDC2-AS1" "LEFTY1" "RP11-1252I4.2"
## [9] "RP4-785G19.5" "RP11-20I20.2" "IDH2-DT" "RP11-396B14.2"
## [13] "SYNPO2L-AS1" "RP5-965G21.3" "P2RX7" "CATSPERG"
## [17] "AGFG2" "NKD1" "GAL3ST2" "ADCY8"
## [21] "CFAP251" "ZNF653" "DHRS3" "C2"
## [25] "TVP23A" "NAV2" "GNG4" "C7orf61"
## [29] "CCDC30" "TRPV1" "LINC00862" "DISP3"
## [33] "ODAD4" "ARL17B" "RP11-348F1.3" "LINC00342"
## [37] "LINC00884" "LINC01137" "EPCAM-DT" "KCNK15-AS1"
## [41] "RP11-60A24.3" "CTD-2189E23.1" "RP11-465L10.14" "RP11-125C10.1"
## [1] 3
## [1] "NRXN3" "RPH3A" "PEX5L" "UNC13A"
## [5] "CALY" "NDST3" "GRIK2" "FSTL5"
## [9] "NRG4" "MTSS1" "GRIK1" "NEGR1"
## [13] "ERICH3" "CCSER1" "NAP1L3" "CYP4X1"
## [17] "PCLO" "ERC2" "GRM7" "FBXO16"
## [21] "RP11-170M17.1" "MSC-AS1" "CXXC4-AS1" "LINC02217"
## [25] "RP4-809F18.1" "RP11-413N10.3" "RP11-640F22.1" "RP11-320L2.1"
## [29] "RP11-335E8.3" "RIMS1" "SEC14L5" "PDE1A"
## [33] "RIMS3" "NLGN1" "RIMS2" "SYN3"
## [37] "PTPRT" "MMP17" "CYP1B1-AS1" "RP11-147G16.1"
## [41] "LINC01322" "PCAT1" "RP11-4D11.1"
## [1] 4
## [1] "BID" "FAR2" "SRPX" "CLIC5" "CRISPLD1" "EEPD1"
## [7] "MASP1" "FADS2" "PTH1R" "IGFBP7" "HESX1" "METTL2B"
## [13] "TMEM130" "GPC6" "ARHGAP8" "PTPRN" "EBF4" "DOK5"
## [19] "RASL12" "BNIP3L" "KLHL29" "NCAN" "GFPT2" "ARID5B"
## [25] "KCNE4" "MYO1E" "SPTBN4" "OXR1" "ABCA3" "KIF5C"
## [31] "CLIC4" "IFFO2" "NPAS2" "PFKFB3" "FRMD5" "RGMA"
## [37] "DUSP8" "ZBTB7C" "TRDN" "RASGEF1A" "RNF208"
## [1] 5
## [1] "MAMLD1" "HHAT" "AHRR" "MROH8"
## [5] "PEBP4" "EFCAB11" "GULP1" "KIAA1328"
## [9] "ZBTB44-DT" "CASC2" "RFLNA" "COL25A1"
## [13] "RFX8" "FIRRE" "LIPE-AS1" "LINC02649"
## [17] "AC105760.2" "TARID" "AC008269.2" "COX10-AS1"
## [21] "RP11-550I24.2" "DRAIC" "CTB-161M19.4" "LINC02615"
## [25] "RP11-266O8.1" "SPESP1" "RP11-111A21.1" "CRTC3-AS1"
## [29] "GEMIN7-AS1" "PLS3-AS1" "RP11-96C13.1" "RP4-681L3.3"
## [33] "NIPAL3" "DOCK10" "NRG2" "FAAH2"
## [37] "TMEM229B" "WARS2-AS1" "LINC01135" "DPH6-DT"
## [41] "AC079610.1" "RP11-379B18.8" "RP11-799O21.2"
## [1] 6
## [1] "SNCAIP" "MAOB" "SEMA3A" "SYTL4"
## [5] "IQCH" "DPYSL3" "TACR1" "LEPR"
## [9] "ACAT2" "COL4A2" "ABI3BP" "PRTG"
## [13] "VWA3B" "HEG1" "PROS1" "F5"
## [17] "LRRC24" "RNF19A" "SEMA3C" "PIR"
## [21] "SPAG1" "FGL1" "ST8SIA1" "MAN1A1"
## [25] "UST" "SERPINI2" "PRRX1" "COL21A1"
## [29] "PRR12" "FCHO1" "COL6A2" "LMNTD1"
## [33] "SEMA3D" "DPYSL5" "ELAPOR2" "TMC1"
## [37] "NPNT" "ZFP36L1" "CPEB1" "RP11-190P13.2"
## [41] "CTD-2054N24.2"
## [1] 7
## [1] "CAP2" "TACC2" "FAXC"
## [4] "LMOD1" "NXN" "SLC43A2"
## [7] "CCBE1" "C9orf153" "TRMT9B"
## [10] "MAP3K9" "GTF2IRD1" "HDAC9"
## [13] "PDZD4" "MYO9B" "SYT17"
## [16] "ARHGEF18" "AEBP1" "WASF1"
## [19] "PACRG" "IL1R1" "ZC4H2"
## [22] "HIP1" "ZBTB46" "IRAK2"
## [25] "KIAA0513" "CCDC40" "MVB12A"
## [28] "CLVS2" "RHPN1" "TMCO4"
## [31] "PIK3CD" "MOB3A" "HAP1"
## [34] "RILPL1" "COL27A1" "NHSL2"
## [37] "MEF2B" "LYRM4" "RP11-513I15.6"
## [40] "FBXO17" "DGCR5_ENSG00000273032" "CASTOR2"
## [1] 8
## [1] "ZFR2" "ST6GALNAC5" "CABLES1" "ABHD3"
## [5] "ANKRD33B" "ADRA1B" "HOPX" "TAFA1"
## [9] "SLIT1" "SULT1A2" "PPP1R26-AS1" "RP11-390F4.6"
## [13] "RP11-380P13.1" "MTRNR2L8" "AC005786.7" "ADGRL1"
## [17] "TRHDE" "CACNA1I" "XYLT1" "PADI2"
## [21] "TGIF2" "TICAM1" "RAP1GAP2" "RHBDL3"
## [25] "ADAMTS10" "ST3GAL2" "CSDC2" "GNG7"
## [29] "CTD-2527I21.15" "SPACA6" "OSBP2" "NOTUM"
## [33] "AJAP1" "NRSN2-AS1" "HPN-AS1" "AC004951.6"
## [37] "HMGA1P4" "RP5-827C21.2" "RP11-346L1.2" "LINC02356"
## [41] "RP3-414A15.10" "MAFG-DT" "ATP6V0D1-DT" "RP11-514P8.10"
## [1] 9
## [1] "EPHA6" "ENOX1" "UNC79" "TMEM132B"
## [5] "C4orf19" "MN1" "ANO5" "MACROD2"
## [9] "LRRC3B" "APTR" "LCNL1" "AP001628.6"
## [13] "RP11-498J9.2" "OBI1-AS1" "RP11-410D17.2" "CTC-329D1.2"
## [17] "LINC01950" "RP11-582J16.4" "LINC00923" "MGAM"
## [21] "RP11-524F11.2" "CTD-2349P21.11" "RP11-437L7.2" "RP11-1289C17.1"
## [25] "RP11-215I16.3" "ATP1A2" "RNF24" "TENM2"
## [29] "ENOX2" "ZMAT3" "ARPP21" "EFNA5"
## [33] "PLK5" "TPCN1" "C3orf35" "RP11-305L7.3"
## [37] "KCNMB2-AS1" "RP5-921G16.1" "LINC01252" "RP11-298I3.1"
## [41] "AGBL1" "RP11-711K1.8"
## [1] 10
## [1] "TRPM3" "GALNT16" "EFEMP1" "GTDC1" "TMEM108" "CXCL14"
## [7] "ACSL1" "WIF1" "VWCE" "TMEM51" "RNLS" "KLHL32"
## [13] "BRINP2" "RARB" "TGFB2" "PALM" "MYOM1" "EEF2K"
## [19] "KAT8" "PPP1R13L" "ISYNA1" "PPARGC1A" "TPD52L1" "TFDP2"
## [25] "B4GALT2" "FOXO3" "SLC39A11" "VAV3" "CCNH" "TIAM2"
## [31] "FAM171A1" "ZEB1" "CNNM2" "FOXO1" "FAM107A" "ZNF608"
## [37] "CRADD" "TCAP" "PARVA" "ZNF358" "EFCAB2" "EML6"
## [1] 11
## [1] "CD38" "REEP1" "SP140" "ANKRD7"
## [5] "PLAGL1" "H3-3B" "BEND6" "BTG2"
## [9] "VWA3A" "PLD5" "PRELID2" "SLC4A5"
## [13] "LGALSL-DT" "LINC01630" "RP11-106M7.1" "LINC00407"
## [17] "CDKN2B-AS1" "BAALC-AS1" "LINC02234" "C5orf17"
## [21] "OSMR-AS1" "RP11-157I4.4" "MPPED2-AS1" "RP11-363J20.2"
## [25] "RP11-798K3.2" "LINC00907" "CTC-513N18.6" "RP11-355F16.1"
## [29] "LINC01374" "ARRDC3-AS1" "BCL6-AS1" "CTD-2313D3.2"
## [33] "RP11-125D12.3" "RP11-592G13.2" "RP11-341N18.1" "TLE2"
## [37] "USP9Y" "PDPN" "NLGN4Y" "TTTY14"
## [41] "UTY" "TTTY10" "RP5-1198O20.4" "LINC00278"
## [1] 12
## [1] "KIRREL3" "GALNTL6" "LINC00326" "KIF5C-AS1"
## [5] "CTD-2126E3.6" "SYT7" "KLHL4" "ATRNL1"
## [9] "SCN2A" "UNC13C" "AK7" "CBLN2"
## [13] "SLC4A10" "CDH18" "CNTN5" "ZNF385D"
## [17] "SLC24A2" "CFAP161" "SHROOM4" "LRRC2"
## [21] "HTR1E" "SLC38A11" "SEMA3E" "SLC8A1"
## [25] "KCNH7" "RTN4RL1" "PDE2A" "CACNA1E"
## [29] "TNFRSF25" "AC023469.1" "RP11-191L9.4" "RP1-30E17.2"
## [33] "RP11-563D10.1" "KRTAP5-AS1" "AC067956.1" "SHISA9"
## [37] "AC002066.1" "CTC-340A15.2" "LINC02223" "RP11-79E3.2"
## [41] "RP11-624C23.1" "RP11-958J22.1" "RP11-596C23.6" "IQCJ-SCHIP1"
## [1] 13
## [1] "ATP11A" "MAP2K6" "MGAT3" "PRR5L" "FAM117B"
## [6] "SLC44A3" "C4orf45" "PBX3" "LRRN2" "CTA-292E10.6"
## [11] "HGF" "SAMD4A" "APBA2" "CDON" "PDK3"
## [16] "TMEM38A" "ITPKC" "RELB" "OLFM2" "PLIN3"
## [21] "RFTN1" "ZSWIM4" "NFIC" "ENSA" "BOC"
## [26] "ZNF208" "FBXO27" "SHISA5" "PKNOX2" "FRMD3"
## [31] "SYT12" "PACS1" "CMTM4" "DMWD" "TCEA3"
## [36] "LINC00685" "RP5-864K19.4" "L3MBTL2-AS1" "OLMALINC" "RP1-158P9.2"
## [41] "MIR23AHG" "RP11-404C6.6"
## [1] 14
## [1] "UPP2" "MOGAT1" "DPH6" "CD72"
## [5] "MAP3K7CL" "RHCE" "CRPPA" "POT1-AS1"
## [9] "LNC-LBCS" "LINC01185" "MIR181A1HG" "MMADHC-DT"
## [13] "RP11-120D5.1" "RPL34-DT" "NPIPB2" "SUCLG2-AS1"
## [17] "RP11-11N9.4" "RP11-130F10.1" "RP11-268P4.5" "RP11-284M14.1"
## [21] "LINC01182" "MAILR" "RP11-156K13.1" "RP11-20E24.1"
## [25] "RP11-397A16.1" "RP11-436D23.1" "RP11-281A20.2" "RP11-382N13.7"
## [29] "RP11-692P14.1" "RP11-444C24.1" "RP11-563M4.2" "CTD-2297M2.1"
## [33] "STAG1" "PDE3A" "LSMEM2" "AP000318.2"
## [37] "LINC00598" "AC104088.1" "ARHGEF26-AS1" "STX18-AS1"
## [41] "CASC17" "TAPT1-AS1" "RP11-26L21.1" "RP11-166M16.1"
## [1] 15
## [1] "PRKAR2B" "ARHGAP44" "TENM1" "ELAVL2" "MLIP" "SETBP1"
## [7] "SHANK2" "RGS7" "KCTD16" "SMYD3" "DLGAP2" "SYT1"
## [13] "RBFOX1" "UBE2R2" "ZMIZ1" "CPE" "HIVEP3" "QRICH2"
## [19] "DPP6" "SOX5" "TTLL7" "ZNF385B" "DIAPH2" "CACNA1B"
## [25] "SHANK1" "ABLIM2" "RBFOX3" "FRMPD4" "DLGAP1" "CNTNAP2"
## [31] "SAMD12" "RGS6" "CSMD1" "OPCML" "RALYL" "KCNQ5"
## [37] "KCNIP4" "ELAVL3" "ARID5A" "RYR2" "MEG3"
## [1] 16
## [1] "XK" "MAEL" "PAH" "GPR39"
## [5] "CC2D2B" "DCHS2" "DIO2" "RP11-306O13.1"
## [9] "AP000233.4" "LINC01117" "PLCG1-AS1" "AC012593.1"
## [13] "SOX21-AS1" "LINC01344" "AC007682.1" "LINC01937"
## [17] "AC009264.1" "RP11-142A5.1" "AC079305.11" "RP11-154H17.1"
## [21] "RP11-373N22.3" "LINC02144" "RP11-669M16.1" "RP11-679C8.2"
## [25] "RP11-404I7.2" "RP1-84O15.2" "LINC00534" "ZFHX4-AS1"
## [29] "RP11-804N13.1" "RP11-541P9.3" "RP11-431M3.1" "LINC02763"
## [33] "RMST" "RP11-260G13.1" "RP11-526N18.1" "RP11-242P2.1"
## [37] "CTC-498M16.4" "RP11-561I11.4" "LINC01727" "CH17-174L20.1"
## [41] "RP11-313M3.2" "RP3-383B8.1" "RP11-346I3.7" "AC006296.4"
## [45] "RP11-399K19.1"
## [1] 17
## [1] "MBNL3" "GABRA4" "HSD11B1" "HS3ST3B1" "GPNMB" "ABCA12"
## [7] "ARHGAP27" "AXDND1" "AGBL2" "ZCCHC18" "EPHX4" "C1QTNF4"
## [13] "SP140L" "WNT7B" "HES5" "L3MBTL3" "SAMD13" "BAALC-AS2"
## [19] "PDXP" "DCN" "ABCA7" "ZFY" "ANGPT2" "PCDH11Y"
## [25] "TNNT2" "TBX2" "AIF1L" "EDA2R" "C1QL1" "SLC6A6"
## [31] "FREM2" "KCNJ16" "CATIP" "SPATA2L" "ZER1" "LRRC8C"
## [37] "NXNL1" "MB21D2" "PCP4" "ETV5"
## [1] 18
## [1] "PNPLA3" "LYPD6B" "DPP10" "CNTN1" "RIMBP2" "CTNNA2"
## [7] "CAB39L" "TUSC3" "GLIS3" "CHRNE" "CLNK" "SGK1"
## [13] "PLXDC2" "HIF3A" "AHNAK" "GALNT8" "RIN2" "ARHGEF4"
## [19] "PLCE1" "SSH2" "BCAS3" "GABPB2" "KCNN3" "DOCK11"
## [25] "ITPRIP" "GRIK4" "RASSF3" "NCAM2" "ABR" "ZNF704"
## [31] "ABCA1" "WNK2" "SLC20A2" "FAM222B" "SH3PXD2B" "PPM1E"
## [37] "PHYHD1" "SWI5" "TSHZ2" "NHS" "SRGAP1" "S100A10"
## [43] "NEAT1"
## [1] 19
## [1] "WDR64" "GLIPR1L1" "FSIP2" "ANKUB1"
## [5] "RNF212B" "AC002463.3" "RP11-131L23.1" "RP4-660H19.1"
## [9] "RP11-547I7.1" "ST7-AS2" "ASTN2-AS1" "RP11-141A19.1"
## [13] "CCDC192" "GPC5-AS2" "PCDH9-AS4" "RP11-666F17.1"
## [17] "LINC02250" "AC008067.2" "RP11-475C16.2" "RP13-143G15.4"
## [21] "LINC02877" "LINC00960" "RP11-768G7.3" "RP11-115N4.1"
## [25] "LRP4-AS1" "ANK2-AS1" "RP11-223C24.1" "MAPK10-AS1"
## [29] "RP11-120A1.1" "RP11-116O11.1" "RP11-351A11.1" "RP11-463D19.1"
## [33] "RP11-513G19.1" "A2ML1-AS1" "RP11-370I10.2" "RP11-887P2.5"
## [37] "DIO2-AS1" "RP11-58G13.1" "RP11-138H11.1" "CTD-2282P23.2"
## [41] "CH17-140K24.2" "RP11-576O3.1" "RP11-394G3.3" "RP11-66G15.1"
## [1] 20
## [1] "PAPPA2" "MTERF1" "PKIB" "SAXO1"
## [5] "PKD1L1" "FREM1" "SCN11A" "RNF212"
## [9] "CLDN4" "SCOC-AS1" "LEKR1" "RP11-344B5.2"
## [13] "AC072062.3" "LINC00271" "RFX3-AS1" "AF131217.1"
## [17] "LINC01239" "LINC01524" "RP11-195C7.1" "LINC01376"
## [21] "LINC01695" "LINC02652" "RP11-132E11.2" "LINC01358"
## [25] "RP11-624M8.1" "H2AZ1-DT" "LINC02355" "LINC01340"
## [29] "LIX1-AS1" "C8orf37-AS1" "RP11-708B6.2" "RP11-511B23.2"
## [33] "RP11-352M15.1" "LINC02320" "RP11-16B13.1" "RP11-739G5.1"
## [37] "PSMD7-DT" "RP11-571L19.7" "RP11-157E16.1" "CTC-490G23.6"
## [41] "RP11-964E11.3" "RP11-274G22.1" "RP11-221G19.1" "RP5-892C22.1"
## [45] "RP11-446J8.1"
## [1] 21
## [1] "CALCRL" "CCDC80" "PLCB4" "SLC16A6"
## [5] "IFI44L" "SLC24A4" "ADAMTS9" "GUCY1A1"
## [9] "DELEC1" "CYP4F12" "CYP4F3" "STUM"
## [13] "INSYN2B" "RP11-735G4.1" "LINC01515" "LINC01768"
## [17] "DIRC3-AS1" "AC007563.5" "AC092684.1" "SOCS2-AS1"
## [21] "NEUROG2-AS1" "VCAN-AS1" "LINC02715" "MAP1LC3B2"
## [25] "RP11-116N8.1" "FRMD6-AS2" "PTCSC3" "DISC1FP1"
## [29] "RP11-793A3.2" "RP11-354K4.2" "RP11-323P17.2" "RP11-290O12.2"
## [33] "LINC00836" "LINC00842" "RP11-364P22.4" "RP11-373E16.6"
## [37] "RP11-259G3.1" "RP11-154D6.3" "RP11-609L3.3" "RP1-20N4.2"
## [41] "RP11-423B13.1" "RP11-469A15.2" "RP11-114N1.1"
## [1] 22
## [1] "PRKCQ" "SDK2" "CEMIP" "GBE1" "AKAP12"
## [6] "EPSTI1" "GALNT10" "STOX2" "CA8" "EXT1"
## [11] "CMSS1" "GCNT1" "TENM3" "MALAT1" "MCF2L2"
## [16] "PLXNA2" "KIF3C" "HSD17B14" "PCSK5" "NAMPT"
## [21] "LIN7A" "ZSWIM6" "ADGRB3" "ARHGAP29" "SLC44A5"
## [26] "PCSK6" "PTPRJ" "ABCB9" "THRB" "JAZF1"
## [31] "ADORA1" "PCDH7" "ALK" "CADM2" "NCKAP5"
## [36] "SLC25A20" "CADM1" "ABAT" "ARL15" "DNM3"
## [41] "TMEM161B-AS1"
## [1] 23
## [1] "CPED1" "BICC1" "SLC14A1"
## [4] "UNC5D" "LRRIQ3" "LINC01266"
## [7] "LMCD1-AS1" "AC097721.2" "LINC00877"
## [10] "RFX2" "SLC26A3" "DAAM1"
## [13] "CDH20" "STEAP1B" "LGI1"
## [16] "RFX4" "LRMDA" "PLCL2"
## [19] "GPR176" "GSG1L" "IQCK"
## [22] "PPP1R42" "APOLD1" "FIGN"
## [25] "LHFPL6" "MAML2" "FLRT2"
## [28] "FAM174B" "NKAIN2" "KIF9-AS1"
## [31] "LINC01320" "RP11-154D17.1" "RP11-17A1.3"
## [34] "LINC02742" "LINC01609" "RP11-20D14.3"
## [37] "RPPH1_ENSG00000259001" "LINC00558" "RP11-838N2.5"
## [40] "RMRP_ENSG00000269900" "CH507-528H12.1" "RP4-799O8.1"
## [43] "AC003099.2" "RP11-398J12.1"
## [1] 24
## [1] "CDH10" "EPB41L4B" "SCG3" "DHRS7B"
## [5] "SLC1A2" "DNAH7" "C10orf90" "MTCL1"
## [9] "SNTB1" "TMEM132C" "ROR1" "SHISA6"
## [13] "RP11-496B10.6" "ARHGAP31" "COL23A1" "RRP12"
## [17] "SYNE2" "DGKG" "SESN1" "PHACTR3"
## [21] "COBL" "CPEB3" "C1orf21" "WLS"
## [25] "PDZRN3" "TOX2" "TNS3" "SLC22A23"
## [29] "SHROOM3" "GLTP" "MAPK4" "SDK1"
## [33] "FAM13C" "ADAM33" "DOC2A" "PID1"
## [37] "GNA14" "AHCYL2" "CACNB2" "ZFPM2"
## [41] "ZNF785" "TOX"
## [1] 25
## [1] "PUDP" "RERG" "OTOGL" "SGCD"
## [5] "SLC24A3" "GRM3" "AC074391.1" "SOX1-OT"
## [9] "EPS15-AS1" "AP000282.2" "LINC01934" "LINC00886"
## [13] "HS3ST5" "LINC02196" "F11-AS1" "LINC00499"
## [17] "LINC01301" "RP11-317N12.1" "GS1-57L11.1" "RP11-134O21.1"
## [21] "LINC00540" "RP11-378A12.1" "RP11-624A4.2" "COL5A3"
## [25] "GRK3" "HPSE2" "CALCB" "FZD8"
## [29] "NME9" "ZNF98" "AC064875.2" "AC003991.3"
## [33] "SPRY4-AS1" "AC002127.4" "PDYN-AS1" "MEIKIN"
## [37] "RTL9" "ALDH1L1-AS2" "LINC02208" "LINC01414"
## [41] "RP11-328J6.1" "RP11-237N2.1" "RP11-421A16.1" "RP11-183J19.1"
## [1] 26
## [1] "IL7" "CA1" "LINC01931" "SHOC1"
## [5] "FILIP1L" "P2RY14" "HEPN1" "TMLHE-AS1"
## [9] "AC105461.1" "AC017101.10" "RP11-417B4.2" "GNA14-AS1"
## [13] "RP11-46O21.2" "GRM3-AS1" "LINC00513" "AC037445.1"
## [17] "RP11-109I13.2" "RBMS3-AS3" "STARD13-AS" "GS1-433O24.1"
## [21] "LINC01877" "RP11-657O9.1" "ZBTB20-AS5" "GK-AS1"
## [25] "RP11-274H2.2" "RORA-AS1" "LUCAT1" "RP11-39E3.3"
## [29] "ZFPM2-AS1" "STPG2-AS1" "CTD-3239E11.2" "BBOX1-AS1"
## [33] "CTD-2537O9.1" "RP11-1H15.2" "AP000462.2" "RP11-315E17.1"
## [37] "RP11-39M21.1" "CRIM1-DT" "PRKCA-AS1" "RP11-555K12.4"
## [41] "SLC5A11" "LINGO1" "LINC01208" "AC013463.2"
## [1] 27
## [1] "FAM107B" "SLC22A3" "RNF150" "LINC01876"
## [5] "XIST" "LINC02884" "CTXND1" "RP11-175O15.1"
## [9] "RASGRP2" "ARHGAP15" "RIPOR2" "TFCP2L1"
## [13] "ACVR1C" "SEM1" "IQCA1" "DMGDH"
## [17] "LGR6" "MRAS" "ESYT3" "VWA5B1"
## [21] "RFTN2" "RANBP3L" "PTCHD1" "FAXDC2"
## [25] "CHST11" "LDLRAD3" "SLC25A18" "POTEG"
## [29] "NWD1" "OSTN" "TMEM184B" "PLIN5"
## [33] "STARD10" "LINC00511" "DLEU2" "PTCHD1-AS"
## [37] "AC016745.3" "RP11-507B12.2" "RP11-507B12.1" "MTRNR2L12"
## [41] "CH507-513H4.1" "LINC02246" "RP11-358F13.1" "RP1-166D18.1"
## [1] 28
## [1] "WNT5B" "PDE10A" "F3" "GDAP1L1"
## [5] "TMEM241" "PDE5A" "MEGF11" "HHIP"
## [9] "SEPTIN1" "PNMA3" "SGCZ" "EYS"
## [13] "HES4" "NPSR1-AS1" "KCNMB2" "RP1-292B18.4"
## [17] "SNAP25-AS1" "RP1-45C12.1" "LINC01829" "LINC01618"
## [21] "RP11-673E1.1" "RP11-586K2.1" "AB015752.3" "LINC02389"
## [25] "LINC02254" "RP11-103J8.1" "RP11-314E10.1" "USH2A"
## [29] "RHOBTB1" "LAMB4" "WFDC1" "PXDNL"
## [33] "GREM1" "MRGPRF" "ZNF804B" "FZD9"
## [37] "HRAT92" "LINC02869" "RP11-384F7.1" "LINC01619"
## [41] "CEACAM16-AS1" "PKD1L3" "RP11-93B21.2"
## [1] 29
## [1] "PON3" "TENT5A" "AGBL3" "SLC9B1"
## [5] "C12orf42" "CATSPERE" "LINC01006" "RANBP17"
## [9] "COL28A1" "AC026188.1" "RP1-15D23.2" "HDAC2-AS2"
## [13] "PCDH9-AS2" "LINC01277" "CCDC26" "UFL1-AS1"
## [17] "PPP1R9A-AS1" "RNF217-AS1" "PKN2-AS1" "RP11-4B14.3"
## [21] "RP5-1101C3.1" "PTPRG-AS1" "NECTIN3-AS1" "RP11-167H9.4"
## [25] "MEF2C-AS2" "LINC00504" "RP11-436F23.1" "RP11-649G15.2"
## [29] "RP11-624D11.2" "CENATAC-DT" "PRANCR" "RP11-72M17.1"
## [33] "LINC01579" "RP11-525K10.3" "LINC01572" "TSIX"
## [37] "LINC02664" "RP11-470M1.2" "RP11-57G22.3" "RP11-69G16.2"
## [41] "RP4-660H19.2" "RP1-84D21.2" "RP11-120J1.2" "RP11-168F16.1"
## [1] 30
## [1] "PHACTR2" "FHAD1"
## [3] "HS3ST3A1" "PCED1B"
## [5] "RP1-167A14.2" "APP-DT"
## [7] "SLCO1A2" "CLIP2"
## [9] "JHY" "BEST3"
## [11] "PATJ" "TMTC1"
## [13] "TTC9" "DGKB"
## [15] "GMPR" "DENND2A"
## [17] "CCDC3" "LRGUK"
## [19] "DRC1" "ORAI2"
## [21] "SYTL3" "ADCY1"
## [23] "ARMC3" "DEPP1"
## [25] "PDZRN4" "TEKT1"
## [27] "ATOH8" "COL24A1"
## [29] "RCAN2" "PRIMA1"
## [31] "SPATA13_ENSG00000182957" "SHTN1"
## [33] "CFAP54" "LINC00632"
## [35] "S1PR3" "AC003090.1"
## [37] "AP001347.6" "AL163953.3"
## [39] "LINC02315" "LINC01094"
## [41] "ZNF594-DT" "KLF2-DT"
## [43] "RP11-35G9.5" "SCARNA2_ENSG00000270066"
## [45] "RP11-154H23.4"
## [1] 31
## [1] "NTN1" "SEZ6L" "SLC39A14" "RGS4" "TRIM5"
## [6] "TESPA1" "RNF165" "PLK2" "ARHGAP18" "PLEKHG4B"
## [11] "MMP16" "SYNPR" "FABP5" "KCNB2" "STAC3"
## [16] "PIWIL2" "AC011288.2" "KCNG1" "CDH3" "CELF4"
## [21] "SLC7A5" "MPP6" "TSPAN11" "NRP2" "SPP1"
## [26] "HS3ST2" "PMEPA1" "LOXL1" "SRRM4" "KCNH5"
## [31] "ITPR1" "RIT2" "FGF17" "PTMS" "ZMAT4"
## [36] "MAP1A" "VAT1L" "NABP1" "ST8SIA3" "VSTM2B"
## [41] "MTRNR2L1"
## [1] 32
## [1] "USH1C" "DNAH9" "GAB2" "SH3D19" "PPM1H" "UBE3D"
## [7] "BEX2" "BTBD11" "MIPOL1" "NDUFAF2" "ABTB2" "TSPAN5"
## [13] "ALCAM" "GPR156" "ADAP2" "AQP1" "SLC7A2" "PDE4A"
## [19] "ATP2B3" "RASAL2" "MAST3" "CDKL1" "COTL1" "SH3PXD2A"
## [25] "ARSB" "TMCC2" "NAV1" "CCDC146" "CDR2" "ITPKB"
## [31] "PAM" "MAGI1" "AKAP6" "ART3" "TIAM1" "GDPD5"
## [37] "ITGA2" "EDIL3" "PLEKHA7" "STX8" "SLC35E3" "ANO6"
## [43] "C19orf38"
## [1] 33
## [1] "CHODL" "STK32A" "BNC2" "LINC02814"
## [5] "RP11-364L4.3" "RP11-492O8.3" "ARHGAP6" "ST6GALNAC2"
## [9] "ST6GAL1" "FAP" "SOHLH2" "LRAT"
## [13] "KLF2" "CCDC175" "ANGPT1" "SAMD3"
## [17] "CFAP47" "PPP1R36" "METTL7B" "CAVIN1"
## [21] "PLCXD3" "SAMD11" "LAMA2" "PLPP4"
## [25] "CFI" "RP11-174G6.1" "RP1-111D6.3" "RP11-146I2.1"
## [29] "RP11-90C4.1" "IQCM" "LINC01411" "LINC01088"
## [33] "RP11-279O9.4" "LINC00609" "LINC02251" "RP11-259K15.2"
## [37] "RP11-627D16.1" "RP11-876N24.2" "RP1-79C4.4" "RP11-403A3.3"
## [41] "RP11-403A3.2" "RP11-542F9.2" "RP11-301F14.1" "RP11-6L16.1"
## [1] 34
## [1] "ASB4" "MSMO1" "CCDC85A" "IDI1" "SRBD1" "BLVRB"
## [7] "PLS3" "RPL18A" "EPM2A" "GMDS" "LAMA4" "ID2"
## [13] "NID1" "PPP1R3C" "MT2A" "ID1" "IFI6" "APOE"
## [19] "RPL36" "CCDC59" "RPLP1" "FAU" "TEX9" "GFRA1"
## [25] "SYCP2L" "HNF4G" "ALDH1A1" "RPS27" "ZNF48" "GINS3"
## [31] "KIAA0825" "MT1X" "PTMA" "SNHG31" "RPS18" "MRPL33"
## [37] "KNOP1" "ARID3A" "CKB" "MITF" "NOL4L"
## [1] 35
## [1] "MRC2" "RIPK2" "NT5DC3" "B3GAT2" "ADCY7" "EPHB2"
## [7] "AVIL" "LPAR4" "CCDC141" "CA3" "SVEP1" "SCG5"
## [13] "PAPPA" "CP" "ATP9A" "FOSL2" "GADD45B" "NFATC2"
## [19] "ABCC3" "IGSF21" "ID3" "ITIH5" "JUND" "EGF"
## [25] "CLSTN3" "DEPTOR" "ARHGAP35" "C1orf87" "ATF3" "TMEM200A"
## [31] "NFIL3" "NT5DC2" "JUNB" "SPSB1" "PLEKHG5" "RND1"
## [37] "PAWR" "YOD1" "FAM110C" "MAFF" "CRYBB2"
## [1] 36
## [1] "BCAS1" "SRPX2" "LRRC9" "LRTM1"
## [5] "CHST9" "CLMP" "MFSD4B" "DLEU1"
## [9] "COL5A2" "TSBP1" "Z83001.1" "RP4-613B23.1"
## [13] "DPP10-AS3" "AC009501.4" "IPO9-AS1" "GNG12-AS1"
## [17] "DPP10-AS1" "RP11-446H18.5" "SEMA6A-AS1" "RP11-114J13.1"
## [21] "CTD-2015H6.3" "RP11-348J24.1" "RP11-517I3.1" "RP11-711G10.1"
## [25] "RP11-452H21.1" "AP000487.6" "RP11-867G2.8" "RP11-144F15.1"
## [29] "RP11-104E19.1" "HIF1A-AS3" "RP11-184D12.1" "AC004158.3"
## [33] "RP11-80I3.1" "SLC7A14-AS1" "CTC-428H11.2" "RP11-589M4.5"
## [37] "RP11-793H13.14" "RP5-847G17.1" "CTD-2172F7.1" "RP11-725F23.1"
## [41] "RP11-255O19.2" "RP11-875G18.1" "NUP210L" "OVCH1"
## [45] "RP11-103P4.1"
## [1] 37
## [1] "ANOS1" "LRRC7" "KCNN2" "DNAH6"
## [5] "RGS22" "KCTD1" "LIX1" "SPATA17"
## [9] "KIF6" "JAM3" "ODAD2" "ENO4"
## [13] "MAML3" "MALRD1" "CHL1-AS2" "PATL2"
## [17] "RP1-232L24.3" "RP1-230L10.1" "CTC-347C20.1" "CTB-178M22.2"
## [21] "ADGRL1-AS1" "LINC00506" "RP11-574F11.4" "RP11-788A4.3"
## [25] "DNAH5" "MOB3B" "CNKSR2" "HNMT"
## [29] "FAM151B" "TDRD9" "FAT3" "SLC26A5"
## [33] "GPR137C" "PAX8-AS1" "TOGARAM2" "TSBP1-AS1"
## [37] "AC092155.4" "RP11-69I8.3" "RP1-35C21.2" "MIR4300HG"
## [41] "RP11-148E17.1" "RP11-210M15.2" "SPANXA2-OT1" "RP11-114N19.3"
## [1] 38
## [1] "MT3" "STS" "MT1G" "SUMF1"
## [5] "C2CD6" "STPG2" "CD200R1" "C11orf65"
## [9] "MT1E" "CYP7B1" "SUGCT" "HMGN5"
## [13] "ADD3-AS1" "MT1H" "AC007277.3" "AC004540.5"
## [17] "LINC00571" "MRPS9-AS2" "RP11-162D16.2" "LYPLAL1-DT"
## [21] "ZRANB2-AS2" "LINC01036" "AC079807.4" "RAP2C-AS1"
## [25] "RP11-154D6.1" "SOX2-OT" "RP11-461O7.1" "C1QTNF7-AS1"
## [29] "RP11-124B13.1" "LINC02740" "RP11-727A23.10" "LINC02745"
## [33] "LINC02326" "LINC02327" "LINC02328" "LINC00637"
## [37] "AC007193.6" "RP11-520F22.1" "KBTBD12" "RP11-26J3.1"
## [41] "RP11-150C16.1" "CTD-2201E18.6" "RP3-466I7.2"
## [1] 39
## [1] "SIDT1" "WSCD2" "ARHGAP28" "SLC8A3"
## [5] "KIAA1549L" "ELL2" "PLXNC1" "RNF175"
## [9] "DUSP15" "DNAAF1" "RETREG1" "GFRA2"
## [13] "SNX31" "DIRC3" "LINC01725" "LINC00958"
## [17] "MAPT-AS1" "MCUB" "BAIAP3" "VCAN"
## [21] "KITLG" "P3H2" "CCL2" "MAN1C1"
## [25] "SCN1A" "ST18" "PARP8" "NFASC"
## [29] "ARHGEF3" "SLITRK5" "FBN1" "TPST1"
## [33] "SLCO3A1" "CHST6" "XXbac-BPG55C20.7" "SATB1-AS1"
## [37] "CTD-2643I7.5" "PTCHD4" "CTB-35F21.1" "LINC02506"
## [41] "RP11-499F3.2" "AF038458.3" "RP5-1015P16.1"
## [1] 40
## [1] "RRAGD" "PSD" "PCSK1N" "POLR2I"
## [5] "RASD1" "PDE8B" "TRIM22" "CHI3L1"
## [9] "FHDC1" "WARS1" "ITGA9" "PRSS23"
## [13] "SPOCK1" "CIITA" "WDR97" "IER5L"
## [17] "CARNMT1-AS1" "RP1-223B1.1" "LINC01503" "PRKAR2B-AS1"
## [21] "RP11-745L13.2" "RP1-41C23.1" "PRAG1" "RP11-239A17.1"
## [25] "CTD-2040G12.2" "GAS7" "KLF6" "FRY"
## [29] "TESC" "DNAH11" "TSHZ3" "HELB"
## [33] "COL5A1" "ADAM12" "SEC24D" "COX7A1"
## [37] "PGM2L1" "CCK" "DPYD" "SLC6A9"
## [41] "SMOC1" "MIR34AHG" "RP1-187B23.1" "RP3-365E2.1"
for(n1 in names(goseq_res)){
k = as.numeric(gsub("set_", "", n1))
print(n1)
print(gene_sets[[k]])
print(goseq_res[[n1]])
}## [1] "set_3"
## [1] "NRXN3" "RPH3A" "PEX5L" "UNC13A"
## [5] "CALY" "NDST3" "GRIK2" "FSTL5"
## [9] "NRG4" "MTSS1" "GRIK1" "NEGR1"
## [13] "ERICH3" "CCSER1" "NAP1L3" "CYP4X1"
## [17] "PCLO" "ERC2" "GRM7" "FBXO16"
## [21] "RP11-170M17.1" "MSC-AS1" "CXXC4-AS1" "LINC02217"
## [25] "RP4-809F18.1" "RP11-413N10.3" "RP11-640F22.1" "RP11-320L2.1"
## [29] "RP11-335E8.3" "RIMS1" "SEC14L5" "PDE1A"
## [33] "RIMS3" "NLGN1" "RIMS2" "SYN3"
## [37] "PTPRT" "MMP17" "CYP1B1-AS1" "RP11-147G16.1"
## [41] "LINC01322" "PCAT1" "RP11-4D11.1"
## $go_bp
## category over_represented_pvalue
## 4455 vesicle mediated transport in synapse 2.919111e-11
## 2093 neurotransmitter secretion 1.324490e-10
## 4266 synaptic vesicle exocytosis 2.667018e-10
## 2094 neurotransmitter transport 1.780282e-09
## 3060 regulated exocytosis 3.286610e-08
## 4130 signal release 3.675377e-07
## 882 exocytosis 7.517528e-07
## 3767 regulation of synaptic vesicle exocytosis 2.592537e-06
## 269 calcium ion regulated exocytosis 4.436216e-06
## 3295 regulation of exocytosis 6.453843e-06
## under_represented_pvalue numDEInCat numInCat FDR
## 4455 1.0000000 10 29 1.310681e-07
## 2093 1.0000000 9 22 2.973480e-07
## 4266 1.0000000 8 16 3.991637e-07
## 2094 1.0000000 9 29 1.998367e-06
## 3060 1.0000000 8 26 2.951376e-05
## 4130 1.0000000 9 54 2.750407e-04
## 882 1.0000000 8 37 4.821957e-04
## 3767 1.0000000 4 6 1.455061e-03
## 269 0.9999999 5 13 2.213179e-03
## 3295 0.9999997 6 23 2.559716e-03
##
## [1] "set_28"
## [1] "WNT5B" "PDE10A" "F3" "GDAP1L1"
## [5] "TMEM241" "PDE5A" "MEGF11" "HHIP"
## [9] "SEPTIN1" "PNMA3" "SGCZ" "EYS"
## [13] "HES4" "NPSR1-AS1" "KCNMB2" "RP1-292B18.4"
## [17] "SNAP25-AS1" "RP1-45C12.1" "LINC01829" "LINC01618"
## [21] "RP11-673E1.1" "RP11-586K2.1" "AB015752.3" "LINC02389"
## [25] "LINC02254" "RP11-103J8.1" "RP11-314E10.1" "USH2A"
## [29] "RHOBTB1" "LAMB4" "WFDC1" "PXDNL"
## [33] "GREM1" "MRGPRF" "ZNF804B" "FZD9"
## [37] "HRAT92" "LINC02869" "RP11-384F7.1" "LINC01619"
## [41] "CEACAM16-AS1" "PKD1L3" "RP11-93B21.2"
## $reactome
## category over_represented_pvalue
## 130 cgmp effects 6.834660e-06
## 607 nitric oxide stimulates guanylate cyclase 1.541836e-05
## under_represented_pvalue numDEInCat numInCat FDR
## 130 1.0000000 3 6 0.007675323
## 607 0.9999999 3 7 0.008657408
##
## [1] "set_34"
## [1] "ASB4" "MSMO1" "CCDC85A" "IDI1" "SRBD1" "BLVRB"
## [7] "PLS3" "RPL18A" "EPM2A" "GMDS" "LAMA4" "ID2"
## [13] "NID1" "PPP1R3C" "MT2A" "ID1" "IFI6" "APOE"
## [19] "RPL36" "CCDC59" "RPLP1" "FAU" "TEX9" "GFRA1"
## [25] "SYCP2L" "HNF4G" "ALDH1A1" "RPS27" "ZNF48" "GINS3"
## [31] "KIAA0825" "MT1X" "PTMA" "SNHG31" "RPS18" "MRPL33"
## [37] "KNOP1" "ARID3A" "CKB" "MITF" "NOL4L"
## $reactome
## category
## 1078 translation
## 287 eukaryotic translation elongation
## 288 eukaryotic translation initiation
## 610 nonsense mediated decay nmd
## 810 response of eif2ak4 gcn2 to amino acid deficiency
## 878 selenoamino acid metabolism
## 856 rrna processing
## 975 srp dependent cotranslational protein targeting to membrane
## 429 influenza infection
## 527 metabolism of amino acids and derivatives
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 1078 1.264399e-07 1.0000000 7 13
## 287 2.368574e-07 1.0000000 6 9
## 288 2.368574e-07 1.0000000 6 9
## 610 2.368574e-07 1.0000000 6 9
## 810 3.470611e-07 1.0000000 6 10
## 878 5.491255e-07 1.0000000 6 10
## 856 6.208334e-07 1.0000000 6 10
## 975 9.426476e-07 1.0000000 6 11
## 429 9.636278e-07 1.0000000 6 11
## 527 1.414785e-06 0.9999999 7 17
## FDR
## 1078 6.649770e-05
## 287 6.649770e-05
## 288 6.649770e-05
## 610 6.649770e-05
## 810 7.794991e-05
## 878 9.959942e-05
## 856 9.959942e-05
## 975 1.202393e-04
## 429 1.202393e-04
## 527 1.588803e-04
##
## $go_bp
## category over_represented_pvalue under_represented_pvalue
## 618 cytoplasmic translation 3.469051e-07 1
## numDEInCat numInCat FDR
## 618 6 12 0.001557604
##
## [1] "set_38"
## [1] "MT3" "STS" "MT1G" "SUMF1"
## [5] "C2CD6" "STPG2" "CD200R1" "C11orf65"
## [9] "MT1E" "CYP7B1" "SUGCT" "HMGN5"
## [13] "ADD3-AS1" "MT1H" "AC007277.3" "AC004540.5"
## [17] "LINC00571" "MRPS9-AS2" "RP11-162D16.2" "LYPLAL1-DT"
## [21] "ZRANB2-AS2" "LINC01036" "AC079807.4" "RAP2C-AS1"
## [25] "RP11-154D6.1" "SOX2-OT" "RP11-461O7.1" "C1QTNF7-AS1"
## [29] "RP11-124B13.1" "LINC02740" "RP11-727A23.10" "LINC02745"
## [33] "LINC02326" "LINC02327" "LINC02328" "LINC00637"
## [37] "AC007193.6" "RP11-520F22.1" "KBTBD12" "RP11-26J3.1"
## [41] "RP11-150C16.1" "CTD-2201E18.6" "RP3-466I7.2"
## $reactome
## category over_represented_pvalue
## 542 metallothioneins bind metals 6.228691e-08
## 813 response to metal ions 6.228691e-08
## under_represented_pvalue numDEInCat numInCat FDR
## 542 1 4 6 3.49741e-05
## 813 1 4 6 3.49741e-05
##
## $go_bp
## category over_represented_pvalue
## 508 cellular response to zinc ion 4.110986e-08
## 677 detoxification of copper ion 4.110986e-08
## 678 detoxification of inorganic compound 4.110986e-08
## 431 cellular response to copper ion 9.843817e-08
## 4029 response to zinc ion 1.945770e-07
## 3900 response to copper ion 2.004453e-07
## 1214 intracellular zinc ion homeostasis 2.040068e-07
## 423 cellular response to cadmium ion 6.392107e-07
## 3891 response to cadmium ion 6.392107e-07
## 676 detoxification 1.864596e-06
## under_represented_pvalue numDEInCat numInCat FDR
## 508 1 4 6 6.152775e-05
## 677 1 4 6 6.152775e-05
## 678 1 4 6 6.152775e-05
## 431 1 4 7 1.104969e-04
## 4029 1 4 8 1.308558e-04
## 3900 1 4 8 1.308558e-04
## 1214 1 4 8 1.308558e-04
## 423 1 4 10 3.188951e-04
## 3891 1 4 10 3.188951e-04
## 676 1 4 13 8.372037e-04Session information
## used (Mb) gc trigger (Mb) limit (Mb) max used (Mb)
## Ncells 8955019 478.3 16112782 860.6 NA 16112782 860.6
## Vcells 16666322 127.2 31263295 238.6 65536 31263295 238.6## R version 4.2.3 (2023-03-15)
## Platform: aarch64-apple-darwin20 (64-bit)
## Running under: macOS Ventura 13.4.1
##
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib
##
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] goseq_1.50.0 geneLenDataBase_1.34.0 BiasedUrn_2.0.10
## [4] fgsea_1.24.0 biomaRt_2.54.1 limma_3.54.2
## [7] tidyr_1.3.0 ggpubr_0.6.0 ggplot2_3.4.2
## [10] data.table_1.14.8
##
## loaded via a namespace (and not attached):
## [1] nlme_3.1-162 matrixStats_1.0.0
## [3] bitops_1.0-7 bit64_4.0.5
## [5] filelock_1.0.2 progress_1.2.2
## [7] httr_1.4.6 GenomeInfoDb_1.34.9
## [9] tools_4.2.3 backports_1.4.1
## [11] bslib_0.4.2 utf8_1.2.3
## [13] R6_2.5.1 mgcv_1.8-42
## [15] DBI_1.1.3 BiocGenerics_0.44.0
## [17] colorspace_2.1-0 withr_2.5.0
## [19] tidyselect_1.2.0 prettyunits_1.1.1
## [21] bit_4.0.5 curl_5.0.1
## [23] compiler_4.2.3 cli_3.6.1
## [25] Biobase_2.58.0 xml2_1.3.4
## [27] DelayedArray_0.24.0 rtracklayer_1.58.0
## [29] sass_0.4.5 scales_1.2.1
## [31] rappdirs_0.3.3 Rsamtools_2.14.0
## [33] stringr_1.5.0 digest_0.6.31
## [35] rmarkdown_2.21 XVector_0.38.0
## [37] pkgconfig_2.0.3 htmltools_0.5.5
## [39] MatrixGenerics_1.10.0 dbplyr_2.3.2
## [41] fastmap_1.1.1 rlang_1.1.0
## [43] rstudioapi_0.14 RSQLite_2.3.1
## [45] BiocIO_1.8.0 jquerylib_0.1.4
## [47] generics_0.1.3 jsonlite_1.8.4
## [49] BiocParallel_1.32.6 dplyr_1.1.2
## [51] car_3.1-2 RCurl_1.98-1.12
## [53] magrittr_2.0.3 GO.db_3.16.0
## [55] GenomeInfoDbData_1.2.9 Matrix_1.6-4
## [57] Rcpp_1.0.10 munsell_0.5.0
## [59] S4Vectors_0.36.2 fansi_1.0.4
## [61] abind_1.4-5 lifecycle_1.0.3
## [63] stringi_1.7.12 yaml_2.3.7
## [65] carData_3.0-5 SummarizedExperiment_1.28.0
## [67] zlibbioc_1.44.0 org.Hs.eg.db_3.16.0
## [69] BiocFileCache_2.6.1 grid_4.2.3
## [71] blob_1.2.4 parallel_4.2.3
## [73] crayon_1.5.2 lattice_0.20-45
## [75] splines_4.2.3 Biostrings_2.66.0
## [77] cowplot_1.1.1 GenomicFeatures_1.50.4
## [79] hms_1.1.3 KEGGREST_1.38.0
## [81] knitr_1.44 pillar_1.9.0
## [83] GenomicRanges_1.50.2 rjson_0.2.21
## [85] ggsignif_0.6.4 codetools_0.2-19
## [87] stats4_4.2.3 fastmatch_1.1-3
## [89] XML_3.99-0.14 glue_1.6.2
## [91] evaluate_0.20 png_0.1-8
## [93] vctrs_0.6.2 gtable_0.3.3
## [95] purrr_1.0.1 cachem_1.0.7
## [97] xfun_0.39 broom_1.0.4
## [99] restfulr_0.0.15 rstatix_0.7.2
## [101] tibble_3.2.1 GenomicAlignments_1.34.1
## [103] AnnotationDbi_1.60.2 memoise_2.0.1
## [105] IRanges_2.32.0